Table 1.
Time and monetary cost breakdown for standard and optimized 16S rRNA sample preparation protocols
| Step | Option | Standard protocol |
Optimized protocol |
||
|---|---|---|---|---|---|
| Hours per 96 samplesa | Cost per 96 samples | Hours per 96 samplesa | Cost per 96 samples | ||
| DNA extraction | Ultra-Clean | 1 | $282 | 1 | $282 |
| Blood and Tissue | 1 | $350 | 1 | $350 | |
| PowerSoil | 2 | $575 | 2 | $575 | |
| DNA quantificationb | 0.25 | $117 | n.n. | ||
| DNA normalization into PCR | 0.5 | $0 | n.n. | ||
| Polymerase for PCR | Platinum II | 3 | $348 | ||
| 5PRIMEc | 3 | $65 | |||
| AccuStart | 3 | $172 | 3 | $57d | |
| PCR clean-up | 0.5 | $180 | 0.5 | $7 | |
| PCR-product quantificationb | 0.25 | $117 | n.n | ||
| Individual sample PCR pool | 0.5 | $0 | 0.125 | $0 | |
| Total | Ultra-Clean w/AccuStart | 6 | $868 | 4.6 | $346 |
| Blood and Tissue w/AccuStart | 6 | $936 | 4.6 | $414 | |
| PowerSoil w/AccuStart | 7 | $1,161 | 5.6 | $639 | |
a
Time calculations assume the use of a semi-automatic 96-well pipetting system.
b
DNA/PCR-product quantification estimates include colorimetric assay reagents and fluorescence 96-well microplates, and assume two replicates per sample. n.n.: not necessary based on the results in this study.
c
5PRIME polymerase has been discontinued, hence AccuStart becomes the best choice for polymerase based on cost.
d
For 25-μL PCRs.